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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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PICRUSt2 Resource Report Resource Website 500+ mentions |
PICRUSt2 (RRID:SCR_022647) | software application, simulation software, software resource | Software for predicting functional abundances based only on marker gene sequences.Used for prediction of metagenome functions. Contains updated and larger database of gene families and reference genomes, provides interoperability with any operational taxonomic unit (OTU)-picking or denoising algorithm, and enables phenotype predictions. Allows addition of custom reference databases. | predicting functional abundances, marker gene sequences, metagenome functions prediction | is related to: PICRUSt | NSF IOS CAREER 1942647; NIDDK U54DK102557; NIDDK R24DK110499; NSERC ; GlaxoSmithKline |
PMID:32483366 | Free, Available for download, Freely available | https://github.com/picrust/picrust2 | SCR_022647 | Phylogenetic Investigation of Communities by Reconstruction of Unobserved States | 2026-08-11 09:44:26 | 583 | ||||||
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Pediatric Cancer Data Commons Resource Report Resource Website 1+ mentions |
Pediatric Cancer Data Commons (RRID:SCR_022369) | PCDC | data or information resource, topical portal, portal, disease-related portal | PCDC brings together clinical, genomic, and imaging data from institutions around the world to transform pediatric cancer research and outcomes. Headquartered at University of Chicago, PCDC works with international leaders in pediatric cancers and National Cancer Institute to develop and apply uniform data standards that facilitate collection, combination, and analysis of data from many different sources. PCDC Consortium developes common core data dictionary and common governance structure spanning pediatric cancers neuroblastoma, soft tissue sarcoma, acute myeloid leukemia, acute lymphoblastic leukemia, germ cell tumors, bone tumors, and Hodgkin lymphoma to enable innovative cross disease research as well as set standard for future cancer data commons endeavors. | pediatric cancer, clinical data, genomic data, imaging data, uniform data standards, common core data dictionary, common governance structure, | is related to: University of Chicago; Illinois; USA | pediatric cancer, neuroblastoma, soft tissue sarcoma, acute myeloid leukemia, acute lymphoblastic leukemia, germ cell tumors, bone tumors, Hodgkin lymphoma | Free, Freely available | SCR_022369 | 2026-08-11 09:44:22 | 2 | ||||||||
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Napari Resource Report Resource Website 10+ mentions |
Napari (RRID:SCR_022765) | web service, software resource, data access protocol | Multi dimensional image viewer for Python. Used for browsing, annotating, and analyzing large multi dimensional images. Can be coupled to machine learning and image analysis tools enabling more user friendly automated analysis. | Multi dimensional image viewer, large multi dimensional images, automated analysis | Free, Available for download, Freely available | https://github.com/napari/napari, https://zenodo.org/record/6598542#.YykVuHbMK3A | SCR_022765 | 2026-08-11 09:44:28 | 46 | ||||||||||
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multiHiCcompare Resource Report Resource Website 1+ mentions |
multiHiCcompare (RRID:SCR_022368) | data analysis software, data processing software, software resource, software application | Software package for removing biases across multiple Hi-C datasets. Properly handles Hi-C-specific decay of chromatin interaction frequencies with increasing distance between interacting regions. | detecting priori known chromatin interaction differences, jointly normalized datasets, recover loss of chromatin interactions, Hi-C specific decay of chromatin interaction frequencies, remove bias between multiple Hi-C datasets | American Cancer Society ; NIEHS T32ES007334 |
DOI:10.1093/bioinformatics/btz048 | Free, Available for download, Freely available | https://github.com/dozmorovlab/multiHiCcompare | SCR_022368 | 2026-08-11 09:44:18 | 4 | ||||||||
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University of Pennsylvania Perelman School of Medicine Penn Medicine BioBank Core Facility Resource Report Resource Website 10+ mentions |
University of Pennsylvania Perelman School of Medicine Penn Medicine BioBank Core Facility (RRID:SCR_022415) | PMBB | service resource, material storage repository, storage service resource, core facility, access service resource, biobank | BioBank supports researchers by providing centralized access to large number of annotated blood and tissue samples. | USEDit, ABRF, annotated blood and tissue samples | is listed by: ABRF CoreMarketplace | ARBF_1421 | https://coremarketplace.org?citation=1&FacilityID=1421 | SCR_022415 | University of Pennsylvania Perelman School of Medicine Penn Medicine BioBank | 2026-08-11 09:44:21 | 16 | |||||||
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EZcalcium Resource Report Resource Website 1+ mentions |
EZcalcium (RRID:SCR_022354) | data analysis software, data processing software, software resource, software application | Software package for MATLAB that makes motion correction, segmentation, signal extraction and dimension reduction, analysis, and visualization of calcium imaging data easy to implement. Open source toolbox for analysis of calcium imaging data. | OpenBehavior, neural signal analysis, neural recording, optical imaging, analyze calcium imaging data |
is listed by: OpenBehavior has parent organization: David Geffen School of Medicine at UCLA; California; USA |
DOI:10.3389/fncir.2020.00025 | Free, Available for download, Freely available | https://github.com/porteralab/EZcalcium | SCR_022354 | 2026-08-11 09:44:20 | 3 | ||||||||
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GuPPy Resource Report Resource Website 10+ mentions |
GuPPy (RRID:SCR_022353) | data analysis software, data processing software, software resource, software application | Software Python toolbox that makes fiber photometry data analysis intuitive and light on programming.Used to measure neural activity of freely behaving animals. | OpenBehavior, photometry analysis, neural activity measure, freely behaving animals |
is listed by: OpenBehavior has parent organization: Northwestern University Feinberg School of Medicine; Illinois; USA |
DOI:10.1038/s41598-021-03626-9 | https://github.com/LernerLab/GuPPy | SCR_022353 | Guided Photometry Analysis in Python | 2026-08-11 09:44:21 | 18 | ||||||||
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Adaptive Immune Receptor Repertoire Rearrangement Schema Resource Report Resource Website 1+ mentions |
Adaptive Immune Receptor Repertoire Rearrangement Schema (RRID:SCR_022592) | portal, topical portal, data or information resource, narrative resource, standard specification | Part of AIRR Data Model, defines annotations needed for rearrangements, which are sequences describing rearranged adaptive immune receptor chain (e.g., antibody heavy chain or TCR beta chain). Data for Rearrangement objects are stored as rows in tab delimited file and should be compatible with any TSV reader. Dataset is defined in this context as: TSV file, TSV with companion YAML file containing metadata, or directory containing multiple TSV files and YAML files. | AIRR Data Model, annotations needed for rearrangements, rearranged adaptive immune receptor chain sequences, | is related to: AIRR Data Commons | PMID:29144493 | Free, Freely available | https://fairsharing.org/FAIRsharing.zwjNAh | SCR_022592 | 2026-08-11 09:44:23 | 1 | ||||||||
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OrthoVenn2 Resource Report Resource Website 100+ mentions |
OrthoVenn2 (RRID:SCR_022504) | web service, software resource, data access protocol | Web server for whole genome comparison and annotation of orthologous clusters across multiple species.Works on any operating system with modern browser and Javascript enabled. Used to identify orthologous gene clusters and supports user define species to upload customized protein sequences. Interactive graphic tool which provides Venn diagram view for comparing multiple species protein sequences. | whole genome comparison and annotation, orthologous clusters across multiple species, identify orthologous gene clusters, comparing multiple species protein sequences | National Natural Science Foundation of China | PMID:31053848 | Free, Freely available | SCR_022504 | 2026-08-11 09:44:19 | 288 | |||||||||
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PavCA project Resource Report Resource Website 1+ mentions |
PavCA project (RRID:SCR_022508) | PavCA | portal, topical portal, data or information resource | Project related to tracking behavior. Used to identify subgroups of individuals that differentially attribute incentive value to food cue. Includes apparatus for studying Pavlovian conditioned approach behavior. Customized rat PavCA chambers are constructed based on modular devices purchased from Med-Associates. Code used to operate equipment and collect data was written using Med-Associates’ MEDSTATE programming language. This program is then loaded into Med-PC V operating program, also created by Med-Associates. | Behavior, behavior analysis, Pavlovian conditioning, apparatus, Pavlovian conditioned approach, Instrument, OpenBehavior |
is listed by: OpenBehavior has parent organization: University at Buffalo; New York; USA |
Free, Freely available | SCR_022508 | Pavlovian Conditioned Approach, PavCA | 2026-08-11 09:44:22 | 2 | ||||||||
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Timed pressure control hardware and software for delivery of air mediated distensions in animal models Resource Report Resource Website 1+ mentions |
Timed pressure control hardware and software for delivery of air mediated distensions in animal models (RRID:SCR_022363) | portal, project portal, data or information resource, instrument resource | System uses Arduino microcontroller to control relay module that operates solenoid valve which all sit in 3D printed housing. Solenoid works in conjunction with flowmeter regulator to allow for controlled flow of pressurized air into target. Timing of distensions is controlled via either custom Python based UI, or by triggered TTL pulse.Timed pressure control hardware and software used for delivery of air mediated distensions in animal models. | OpenBehavior, Instrument, behavior apparatus, delivery of air mediated distensions, animal models | is listed by: OpenBehavior | DOI:10.1016/J.OHX.2022.E00271 | Free, Freely available | https://osf.io/rs5p4 | SCR_022363 | Timed pressure control hardware and software for delivery of air mediated distensions in animal models project | 2026-08-11 09:44:20 | 1 | |||||||
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OpenPose Resource Report Resource Website 10+ mentions |
OpenPose (RRID:SCR_022362) | data analysis software, data processing software, software resource, software application | Software tool as multi subject keypoint detection library for real time pose estimation.Used to track behavior of monkeys in natural environments, without disrupting their typical pattern of behavior. Deep learning software system for body, face, hands, and foot estimation in monkeys. | OpenBehavior, tracking limb orientation, behavior measurement, freely moving, realtime recording and analysis, video analysis | is listed by: OpenBehavior | DOI:10.1101/2021.01.28.428726 | Free, Available for download, Freely available | https://github.com/CMU-Perceptual-Computing-Lab/openpose | SCR_022362 | 2026-08-11 09:44:21 | 13 | ||||||||
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TRex Resource Report Resource Website 1+ mentions |
TRex (RRID:SCR_022361) | data analysis software, data processing software, software resource, software application | Open source animal tracking software tool. Used to visually track movement of multiple animals at once. | OpenBehavior, animal tracking, visually track movement | is listed by: OpenBehavior | DOI:10.7554/eLife.64000 | https://github.com/mooch443/trex | SCR_022361 | 2026-08-11 09:44:18 | 2 | |||||||||
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ExonScan Web Server Resource Report Resource Website 1+ mentions |
ExonScan Web Server (RRID:SCR_022516) | web service, software resource, data access protocol | Software framework for modeling sequence motifs based on maximum entropy principle. | modeling sequence motifs, maximum entropy principle | has parent organization: MIT; Cambridge; Massachusetts; United States | PMID:15285897 | Free, Freely available | SCR_022516 | ExonScan | 2026-08-11 09:44:19 | 2 | ||||||||
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ShinyCell Resource Report Resource Website 10+ mentions |
ShinyCell (RRID:SCR_022756) | software application, data processing software, software resource, data visualization software | Software R package to create interactive Shiny based web applications to visualise single cell data via visualising cell information and/or gene expression on reduced dimensions e.g. UMAP, visualising coexpression of two genes on reduced dimensions, visualising distribution of continuous cell information e.g. nUMI / module scores using violin plots / box plots, visualising composition of different clusters / groups of cells using proportion plots and visualising expression of multiple genes using bubbleplots / heatmap.Shiny Interactive Web Apps for Single-Cell Data. | visualise single cell data, visualising cell information, gene expression on reduced dimensions, visualising coexpression of two genes on reduced dimensions, visualising distribution of continuous cell information | works with: Shiny | Free, Available for download, Freely available | SCR_022756 | 2026-08-11 09:44:21 | 24 | ||||||||||
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DLStream Resource Report Resource Website 1+ mentions |
DLStream (RRID:SCR_022359) | data analysis software, data processing software, software resource, software application | Software tool enables closed loop behavioral experiments using deep learning based markerless, real time posture detection.Closed loop behavioral experiment toolkit using pose estimation of body parts. | OpenBehavior, video analysis, behavioral experiment, pose estimation, body parts | is listed by: OpenBehavior | Projekt DEAL | DOI:10.1038/s42003-021-01654-9 | Free, Available for download, Freely available | https://github.com/SchwarzNeuroconLab/DeepLabStream | SCR_022359 | DeepLabStream | 2026-08-11 09:44:21 | 1 | ||||||
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Variational Embedding of Animal Motion Resource Report Resource Website 1+ mentions |
Variational Embedding of Animal Motion (RRID:SCR_022477) | VAME | software application, data processing software, software resource, data visualization software | Software Python tool to cluster behavioral signals obtained from pose estimation tools. Unsupervised probabilistic deep learning framework capable of finding behavioral motifs in pose estimation data. Capable of augmenting quantitative behavioral analyses of data derived from standard pose-estimation software packages. Written based on core functions from DeepLabCut, and readily works with pose data from that package. Can also work with data from other pose estimation packages such as SLEAP. | OpenBehavior, vame, variational embedding of animal motion, pytorch, pose estimation |
is listed by: OpenBehavior is related to: DeepLabCut is related to: SLEAP, LEAP and MotionMapper project |
Free, Available for download, Freely available | https://edspace.american.edu/openbehavior/project/vame/ | SCR_022477 | Variational Animal Motion Embedding, VAME: Variational Embedding of Animal Motion | 2026-08-11 09:44:19 | 3 | |||||||
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ComplexUpset Resource Report Resource Website 10+ mentions |
ComplexUpset (RRID:SCR_022752) | data analysis software, data processing software, software resource, software application | Software R package for visualization of intersecting sets. Used for quantitative analysis of sets, their intersections, and aggregates of intersections. Visualizes set intersections in matrix layout and introduces aggregates based on groupings and queries. | visualization of intersecting sets, set intSections in matrix layout, aggregates based on groupings and queries, quantitative analysis of sets |
uses: ggplot2 is listed by: CRAN |
Austrian Science Fund ; Air Force Research Laboratory and DARPA ; NHGRI K99 HG007583 |
PMID:26356912 | Free, Available for download, Freely available | SCR_022752 | 2026-08-11 09:44:21 | 25 | ||||||||
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ZDOCK Server Resource Report Resource Website 100+ mentions |
ZDOCK Server (RRID:SCR_022518) | web service, software resource, data access protocol | Web tool as protein docking server, based on rigid body docking programs ZDOCK and M-ZDOCK, to predict structures of protein-protein complexes and symmetric multimers. | Protein docking server, ZDOCK, M-ZDOCK, predict structures, protein-protein complexes, symmetric multimers | NIGMS GM084884 | PMID:24532726 | Free, Freely available | SCR_022518 | 2026-08-11 09:44:23 | 137 | |||||||||
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learnMSA Resource Report Resource Website 1+ mentions |
learnMSA (RRID:SCR_022572) | software application, alignment software, image analysis software, software resource, data processing software | Software tool as multiple sequence alignment formulated as statistical machine learning problem, where optimal profile hidden Markov model for potentially very large family of protein sequences is searched and alignment is decoded. | Multiple sequence alignment, protein sequences, statistical machine learning problem, hidden Markov model | Free, Available for download, Freely available | SCR_022572 | 2026-08-11 09:44:25 | 2 |
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